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root/group/trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZ.cpp
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Comparing trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2984 by gezelter, Wed Aug 30 21:04:04 2006 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 54 | Line 54 | using namespace oopse;
54   #include "visitors/RigidBodyVisitor.hpp"
55   #include "visitors/OtherVisitor.hpp"
56   #include "visitors/ZconsVisitor.hpp"
57 + #include "selection/SelectionEvaluator.hpp"
58 + #include "selection/SelectionManager.hpp"
59 + #include "visitors/LipidTransVisitor.hpp"
60 + #include "visitors/AtomNameVisitor.hpp"
61 +
62   using namespace oopse;
63  
64   int main(int argc, char* argv[]){
# Line 63 | Line 68 | int main(int argc, char* argv[]){
68    
69    gengetopt_args_info args_info;
70    std::string dumpFileName;
66 –  std::string mdFileName;
71    std::string xyzFileName;
72    
73    //parse the command line option
# Line 79 | Line 83 | int main(int argc, char* argv[]){
83      exit(1);
84    }
85    
82 –  mdFileName = dumpFileName;
83 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
84 –  
86    if (args_info.output_given){
87      xyzFileName = args_info.output_arg;
88    } else {
# Line 91 | Line 92 | int main(int argc, char* argv[]){
92    
93    //parse md file and set up the system
94    SimCreator creator;
95 <  SimInfo* info = creator.createSim(mdFileName);
95 >  SimInfo* info = creator.createSim(dumpFileName, false);
96    
97 <  
98 <  
98 <  //creat visitor list
97 >
98 >  //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100 –  
101 –  //creat ignore visitor
102 –  if(args_info.ignore_given ||args_info.water_flag){
100      
101 <    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
105 <    
106 <    for(int i = 0; i < args_info.ignore_given; i++)
107 <      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
108 <    
109 <    //ignore water
110 <    if(args_info.water_flag){
111 <      ignoreVisitor->addIgnoreType("SSD");
112 <      ignoreVisitor->addIgnoreType("SSD1");
113 <      ignoreVisitor->addIgnoreType("SSD_E");
114 <      ignoreVisitor->addIgnoreType("SSD_RF");
115 <      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
116 <      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
117 <      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
118 <      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
119 <      ignoreVisitor->addIgnoreType("DPD_RB_0");
120 <    }
121 <    
122 <    compositeVisitor->addVisitor(ignoreVisitor, 1000);
123 <  }
124 <  
125 <  //creat RigidBody Visitor
101 >  //create RigidBody Visitor
102    if(args_info.rigidbody_flag){
103      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104      compositeVisitor->addVisitor(rbCOMVisitor, 900);
105    }
106    
107 <  //compositeVisitor->addVisitor(lipidVisitor, 900);
132 <  
133 <  //creat SSD atom visitor
107 >  //create SSD atom visitor
108    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109    compositeVisitor->addVisitor(ssdVisitor, 800);
110    
111 <  LinearVisitor* linearVisitor = new LinearAtomVisitor(info);
111 >  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112    compositeVisitor->addVisitor(linearVisitor, 750);
113 +  if (args_info.gb_given) {
114 +    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115 +  }
116    
117 <  //creat default atom visitor
117 >  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118 >  compositeVisitor->addVisitor(gbLipidVisitor, 740);
119 >
120 >  //create default atom visitor
121    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
122    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
123    
124 <  //creat waterType visitor
124 >  //create waterType visitor
125    if(args_info.watertype_flag){
126      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
127      compositeVisitor->addVisitor(waterTypeVisitor, 600);
128    }
129 +
130 +  if (args_info.basetype_flag) {
131 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
133 +
134 +  }
135    
136    //create ZconsVisitor
137    if(args_info.zconstraint_flag){
# Line 159 | Line 145 | int main(int argc, char* argv[]){
145      }
146    }
147    
148 <  //creat wrapping visitor
148 >  //create wrapping visitor
149    
150 <  if(args_info.periodicBox_flag){
151 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
153 <  }
154 <  
155 <  //creat replicate visitor
150 >  //if(args_info.periodicBox_flag){
151 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
153 >  //}
154 >
155 >  //create replicate visitor
156    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
157      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
158      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
159      compositeVisitor->addVisitor(replicateVisitor, 300);
160    }
161 <  
162 <  //creat xyzVisitor
163 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
161 >
162 >
163 >  //create rotation visitor
164 >  if (args_info.refsele_given&& args_info.originsele_given) {
165 >    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
166 >  } else if (args_info.refsele_given || args_info.originsele_given) {
167 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
168 >    exit(1);
169 >  }
170 >    
171 >  //create xyzVisitor
172 >  XYZVisitor* xyzVisitor;
173 >  if (args_info.selection_given) {
174 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
175 >  } else {
176 >    xyzVisitor = new XYZVisitor(info);
177 >  }
178    compositeVisitor->addVisitor(xyzVisitor, 200);
179    
180    std::cout << compositeVisitor->toString();
181    
182 <  //creat prepareVisitor
182 >  //create prepareVisitor
183    PrepareVisitor* prepareVisitor = new PrepareVisitor();
184    
185    //open dump file
# Line 197 | Line 197 | int main(int argc, char* argv[]){
197    Molecule* mol;
198    StuntDouble* integrableObject;
199    RigidBody* rb;
200 <  
200 >  Vector3d molCom;
201 >  Vector3d newMolCom;
202 >  Vector3d displacement;
203 >  Mat3x3d hmat;
204 >  Snapshot* currentSnapshot;
205 >      
206    for (int i = 0; i < nframes; i += args_info.frame_arg){
207      dumpReader->readFrame(i);
208 <    
208 >
209 >    //wrapping the molecule
210 >    if(args_info.periodicBox_flag) {
211 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
212 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
213 >          molCom = mol->getCom();
214 >          newMolCom = molCom;
215 >          currentSnapshot->wrapVector(newMolCom);
216 >          displacement = newMolCom - molCom;
217 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
218 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
219 >          integrableObject->setPos(integrableObject->getPos() + displacement);
220 >        }
221 >      }    
222 >    }
223      //update atoms of rigidbody
224      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
225        
# Line 220 | Line 239 | int main(int argc, char* argv[]){
239      
240      //update visitor
241      compositeVisitor->update();
242 <    
242 >
243 >
244      //visit stuntdouble
245      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
246        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 236 | Line 256 | int main(int argc, char* argv[]){
256    
257    xyzStream.close();
258    
259 <  
259 >  delete prepareVisitor;
260    delete compositeVisitor;
261    delete info;
262    

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